Characterization of adaptation mechanisms in sorghum using a multireference back-cross nested association mapping design and envirotyping.

IF 3.3 3区生物学

Genetics Pub Date : 2024-02-21 DOI:10.1093/genetics/iyae003

Vincent Garin, Chiaka Diallo, Mohamed Lamine Tékété, Korotimi Théra, Baptiste Guitton, Karim Dagno, Abdoulaye G Diallo, Mamoutou Kouressy, Willmar Leiser, Fred Rattunde, Ibrahima Sissoko, Aboubacar Touré, Baloua Nébié, Moussa Samaké, Jana Kholovà, Julien Frouin, David Pot, Michel Vaksmann, Eva Weltzien, Niaba Témé, Jean-François Rami

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引用次数: 0

Abstract

Identifying the genetic factors impacting the adaptation of crops to environmental conditions is of key interest for conservation and selection purposes. It can be achieved using population genomics, and evolutionary or quantitative genetics. Here we present a sorghum multireference back-cross nested association mapping population composed of 3,901 lines produced by crossing 24 diverse parents to 3 elite parents from West and Central Africa-back-cross nested association mapping. The population was phenotyped in environments characterized by differences in photoperiod, rainfall pattern, temperature levels, and soil fertility. To integrate the multiparental and multi-environmental dimension of our data we proposed a new approach for quantitative trait loci (QTL) detection and parental effect estimation. We extended our model to estimate QTL effect sensitivity to environmental covariates, which facilitated the integration of envirotyping data. Our models allowed spatial projections of the QTL effects in agro-ecologies of interest. We utilized this strategy to analyze the genetic architecture of flowering time and plant height, which represents key adaptation mechanisms in environments like West Africa. Our results allowed a better characterization of well-known genomic regions influencing flowering time concerning their response to photoperiod with Ma6 and Ma1 being photoperiod-sensitive and the region of possible candidate gene Elf3 being photoperiod-insensitive. We also accessed a better understanding of plant height genetic determinism with the combined effects of phenology-dependent (Ma6) and independent (qHT7.1 and Dw3) genomic regions. Therefore, we argue that the West and Central Africa-back-cross nested association mapping and the presented analytical approach constitute unique resources to better understand adaptation in sorghum with direct application to develop climate-smart varieties.

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利用多参照系回交嵌套关联制图设计和环境类型分析，确定高粱适应机制的特征。

确定影响作物对环境条件适应性的遗传因素是保护和选择作物的关键所在。这可以通过群体基因组学、进化遗传学或数量遗传学来实现。本文介绍了一个高粱多参考回交嵌套关联图谱群体，该群体由来自西非和中非的 24 个不同亲本与 3 个精英亲本杂交产生的 3901 个品系组成--回交嵌套关联图谱。该群体在光周期、降雨模式、温度水平和土壤肥力不同的环境中进行了表型分析。为了整合多亲本和多环境维度的数据，我们提出了一种新的定量性状位点（QTL）检测和亲本效应估计方法。我们对模型进行了扩展，以估计 QTL 效应对环境协变量的敏感性，从而促进了环境类型数据的整合。我们的模型允许在感兴趣的农业生态中对 QTL 效应进行空间预测。我们利用这一策略分析了开花时间和株高的遗传结构，这代表了西非等环境中的关键适应机制。我们的研究结果更好地描述了影响开花时间的著名基因组区域对光周期的反应，其中 Ma6 和 Ma1 对光周期敏感，而可能的候选基因 Elf3 所在区域对光周期不敏感。我们还通过物候依赖基因组区（Ma6）和独立基因组区（qHT7.1 和 Dw3）的共同作用，更好地了解了植株高度的遗传决定性。因此，我们认为西非和中非回交嵌套关联图谱和所介绍的分析方法是更好地了解高粱适应性的独特资源，可直接用于开发气候智能型品种。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genetics 生物-遗传学

CiteScore

6.20

自引率

6.10%

发文量

177

期刊介绍： GENETICS is published by the Genetics Society of America, a scholarly society that seeks to deepen our understanding of the living world by advancing our understanding of genetics. Since 1916, GENETICS has published high-quality, original research presenting novel findings bearing on genetics and genomics. The journal publishes empirical studies of organisms ranging from microbes to humans, as well as theoretical work. While it has an illustrious history, GENETICS has changed along with the communities it serves: it is not your mentor''s journal. The editors make decisions quickly – in around 30 days – without sacrificing the excellence and scholarship for which the journal has long been known. GENETICS is a peer reviewed, peer-edited journal, with an international reach and increasing visibility and impact. All editorial decisions are made through collaboration of at least two editors who are practicing scientists. GENETICS is constantly innovating: expanded types of content include Reviews, Commentary (current issues of interest to geneticists), Perspectives (historical), Primers (to introduce primary literature into the classroom), Toolbox Reviews, plus YeastBook, FlyBook, and WormBook (coming spring 2016). For particularly time-sensitive results, we publish Communications. As part of our mission to serve our communities, we''ve published thematic collections, including Genomic Selection, Multiparental Populations, Mouse Collaborative Cross, and the Genetics of Sex.